JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
Adjuvant radiotherapy in centrally located hepatocellular carcinomas after hepatectomy with narrow margin (<1 cm): a prospective randomized study.
J. Am. Coll. Surg.
PUBLISHED: 02-25-2014
Show Abstract
Hide Abstract
Although radiotherapy (RT) provides potential benefits for patients with hepatocellular carcinomas (HCCs) that are unsuitable for operation, the specific role of adjuvant RT in HCC after hepatectomy remains ill defined. The current study's aim was to evaluate the safety and efficacy of adjuvant RT for centrally located HCCs after narrow-margin (<1 cm) hepatectomy.
Related JoVE Video
Exploration of novel cellular and serological antigen biomarkers in the ORFeome of Mycobacterium tuberculosis.
Mol. Cell Proteomics
PUBLISHED: 01-21-2014
Show Abstract
Hide Abstract
Increasing evidence demonstrates that antigen-specific cellular and humoral immunity plays an indispensable role in protection against Mycobacterium tuberculosis infection. Antigen is a key element in the development of a successful diagnostic method and vaccine. However, few antigens are available, and a systemic study on M. tuberculosis ORFeome-based antigen screening is still lacking. In the current study, a genome-wide examination was conducted on high-throughput M. tuberculosis encoding proteins and novel antigens were identified via a comprehensive investigation of serological and antigen-specific cellular responses. The serological immunoglobulin G level of each protein was detected in pooled sera from 200 pulmonary tuberculosis patients by means of semi-quantitative Western blot. Of the 1,250 detected proteins, 29 were present at a higher level relative to the commercialized 38-kDa protein. Furthermore, the top 12 of the 29 proteins had not been previously reported, and their antigenicity was validated in serum from each individual patient. Results confirmed that the 12 proteins displayed nearly identical immunoglobulin G antibody levels in patients with pulmonary and extrapulmonary tuberculosis. Antigen-specific cellular interferon-? secretion was also evaluated using a cell-based ELISPOT assay. Thirty-four of the proteins were able to induce positive interferon-? production by peripheral blood mononuclear cells from pulmonary tuberculosis patients as judged by positive (commercial ESAT-6 antigen) and negative controls. The top 4 candidates out of the 34 proteins displayed good accuracy ranging from 50% to 80% compared with the commercial ESAT-6 antigen. Subsequent epitope examination confirmed that a pool of peptides, including a 25aa peptide from Rv1198, demonstrated significant tuberculosis-specific cellular interferon-? production. Overall, the current study draws significant attention to novel M. tuberculosis antigens, many of which have not been previously reported. This discovery provides a large amount of useful information for the diagnosis of tuberculosis and the development of vaccines to provide protection against tuberculosis.
Related JoVE Video
Full genome of influenza A (H7N9) virus derived by direct sequencing without culture.
Emerging Infect. Dis.
PUBLISHED: 11-12-2013
Show Abstract
Hide Abstract
An epidemic caused by influenza A (H7N9) virus was recently reported in China. Deep sequencing revealed the full genome of the virus obtained directly from a patients sputum without virus culture. The full genome showed substantial sequence heterogeneity and large differences compared with that from embryonated chicken eggs.
Related JoVE Video
Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy.
BMC Genomics
PUBLISHED: 06-20-2013
Show Abstract
Hide Abstract
Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic approach using mTRAQ labeling to evaluate the expression of specific phosphoproteins during pregnancy comparison with non-pregnancy.
Related JoVE Video
Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry.
Mol. Cell Proteomics
PUBLISHED: 04-24-2013
Show Abstract
Hide Abstract
Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although its efficacy against TB has displayed a high degree of variability (0%-80%) in different trials, Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents. In this study, we performed a proteomic analysis of BCG culture filtrate proteins using SDS-PAGE and high-resolution Fourier transform mass spectrometry. In total, 239 proteins (1555 unique peptides) were identified, including 185 secreted proteins or lipoproteins. Furthermore, 17 novel protein products not annotated in the BCG database were detected and validated by means of RT-PCR at the transcriptional level. Additionally, the translational start sites of 52 proteins were confirmed, and 22 proteins were validated through extension of the translational start sites based on N-terminus-derived peptides. There are 103 secreted proteins that have not been reported in previous studies on the mycobacterial secretome and are unique to our study. The physicochemical characteristics of the secreted proteins were determined. Major components from the culture supernatant, including low-molecular-weight antigens, lipoproteins, Pro-Glu and Pro-Pro-Glu family proteins, and Mce family proteins, are discussed; some components represent potential predominant antigens in the humoral and cellular immune responses.
Related JoVE Video
Co-occurrence of amikacin-resistant and -susceptible Mycobacterium tuberculosis isolates in clinical samples from Beijing, China.
J. Antimicrob. Chemother.
PUBLISHED: 03-28-2013
Show Abstract
Hide Abstract
This study examined the phenomenon of heteroresistance in Mycobacterium tuberculosis clinical isolates obtained from retreated patients in Beijing, China between 2006 and 2011.
Related JoVE Video
Characterisation of a thermo-alkali-stable lipase from oil-contaminated soil using a metagenomic approach.
Syst. Appl. Microbiol.
PUBLISHED: 02-15-2013
Show Abstract
Hide Abstract
Lipases are widely used for a variety of biotechnological applications. Screening these industrial enzymes directly from environmental microorganisms is a more efficient and practical approach than conventional cultivation-dependent methods. Combined with activity-based functional screening, six clones with lipase activity were detected and a gene (termed lipZ01) isolated from a target clone with the highest lipase activity was cloned from an oil-contaminated soil-derived metagenomic library and then sequenced. Gene lipZ01 was expressed in Pichia pastoris GS115 and the molecular weight of the recombinant lipase LipZ01 was estimated by electrophoresis analysis to be approximately 50 kDa. The maximum activity of the purified lipase was 42 U/mL, and the optimum reaction temperature and pH value were 45 °C and 8.0, respectively. The enzyme was highly stable in the temperature range 35-60 °C and under alkaline conditions (pH 7-10). The presence of Ca(2+) and Mn(2+) ions could significantly enhance the activity of the lipase. The purified lipase preferentially hydrolysed triacylglycerols with acyl chain lengths ?8 carbon atoms, and the conversion degree of biodiesel production was nearly 92% in a transesterification reaction using olive oil and methanol. Some attractive properties suggested that the recombinant lipase may be valuable in industrial applications.
Related JoVE Video
Intrahepatic biliary cystadenoma and cystadenocarcinoma: an experience of 30 cases.
Dig Liver Dis
PUBLISHED: 07-26-2011
Show Abstract
Hide Abstract
Intrahepatic biliary cystadenoma and biliary cystadenocarcinoma are extremely rare neoplasms of the liver. They share similar radiological characteristics, and the clinicopathological features are poorly defined. We aim to provide an algorithm for preoperative differentiation of the two diseases.
Related JoVE Video
A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF.
BMC Genomics
PUBLISHED: 05-06-2011
Show Abstract
Hide Abstract
New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition.
Related JoVE Video
Prognostic factors after liver resection for hepatocellular carcinoma: a single-center experience from China.
Am. J. Surg.
PUBLISHED: 05-04-2011
Show Abstract
Hide Abstract
This study aimed to clarify the risk factors for survival and recurrence of hepatocellular carcinoma (HCC) in a cohort of Chinese HCC patients after hepatectomy and to compare 6 developed staging systems.
Related JoVE Video
Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.
BMC Genomics
PUBLISHED: 01-18-2011
Show Abstract
Hide Abstract
Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the worlds total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions.
Related JoVE Video
Combination of liquid hot water pretreatment and wet disk milling to improve the efficiency of the enzymatic hydrolysis of eucalyptus.
Bioresour. Technol.
Show Abstract
Hide Abstract
Combination of liquid hot water pretreatment (LHWP) and wet disk milling (WDM) was investigated in this study to enhance the sugar recovery yield both in prehydrolyzate and enzymatic hydrolyzate. The results show that WDM with LHWP at 180 °C for 20 min produced maximum xylose and glucose yields of 91.62% and 88.12%, respectively, which are higher than that of dilute acid pretreatment or individual LHWP. Corresponding concentration of fermentation inhibitors such as acetic acid, HMF, and furfural in the prehydrolyzate are about 0.98, 0.07 and 0.78 g/L, respectively, which indicated that the detoxification may be not required in the next fermentation step. The acid-insoluble lignin recovery in the insoluble solid resulting from enzymatic hydrolysis, was 25.67/100g raw material, representing 90.7% of acid-insoluble lignin in the eucalyptus biomass. It can be concluded that liquid hot water pretreatment combined with wet disk milling can be successfully applied to eucalyptus.
Related JoVE Video
Elevated pretherapy serum IL17 in primary hepatocellular carcinoma patients correlate to increased risk of early recurrence after curative hepatectomy.
PLoS ONE
Show Abstract
Hide Abstract
Primary hepatocellular carcinoma (HCC) is usually presented in inflamed fibrotic/cirrhotic liver with extensive lymphocyte infiltration. We examined the associations between the HCC early recurrence and alterations in serum levels of inflammatory cytokines.
Related JoVE Video
Molecular cloning and heterologous expression of a true lipase in Pichia pastoris isolated via a metagenomic approach.
J. Mol. Microbiol. Biotechnol.
Show Abstract
Hide Abstract
Lipases are important enzymes for various biotechnological applications. By using functional expression screening, lipZ03, a novel lipase gene, was isolated from a soil-derived metagenomic library. The gene was supposed to encode a protein of 617 amino acids with a C-terminal targeting signal region and four potential N-linked glycosylation sites. The protein sequence shared a conserved GXSXG motif (X represents any amino acid residue) with other microbial lipases. Gene lipZ03 was expressed in Pichia pastoris and the molecular weight was estimated to be approximately 65 kDa by electrophoresis. The optimum reaction temperature and pH value for LipZ03 was 50°C and 9.0, respectively. The enzyme was highly stable in the temperature range of 40-60°C and under alkaline conditions (pH 8-10). Lipolytic activity was significantly enhanced by Ca(2+) and Mg(2+) ions, but dramatically inhibited by Cu(2+), Ni(2+) and Hg(2+) ions and EDTA. The purified enzyme preferentially hydrolyzed relatively long-chain triacylglycerols and was a true lipase rather than an esterase. Using a multi-stepwise methanol supply, the purified LipZ03 achieved a conversion yield of biodiesel production up to 74% after 36 h. Some interesting characteristics described here showed that the recombinant lipase may have potential to be a useful enzyme in industrial applications.
Related JoVE Video
A comprehensive proteomic analysis of Mycobacterium bovis bacillus Calmette-Guérin using high resolution Fourier transform mass spectrometry.
J Proteomics
Show Abstract
Hide Abstract
Since 1921, Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important vaccine to prevent tuberculosis worldwide. Nonetheless, a global analysis of BCG proteome has not been clearly investigated. In this study, we performed an in-depth proteomic analysis of BCG under an in vitro cultivation condition using SDS-PAGE and high resolution Fourier transform mass spectrometry. In total, 3434 proteins (35,259 unique peptides) including 512 transmembrane proteins were identified, covering ~87% of the predicted BCG proteome. Seven pseudogene protein products were also obtained and validated by RT-PCR at gene transcript level. Additionally, translational start sites of 832 proteins were confirmed and 186 were extended using N-terminus-derived peptides. The physicochemical characteristics of all identified proteins were determined. Some predominant proteins, including PE and PPE family proteins, lipoproteins, heat shock proteins, transport proteins and low molecular weight protein antigens, are discussed, which represent potential prominent antigens in the humoral and cellular immune response. This study represents the most comprehensive BCG proteome to date, which will likely facilitate the design of vaccination and immunodiagnostic strategies against TB.
Related JoVE Video
Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces.
J. Virol.
Show Abstract
Hide Abstract
Bats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China. To analyze viromes, we used sequence-independent PCR amplification and next-generation sequencing technology (Solexa Genome Analyzer II; Illumina). The viromes were identified by sequence similarity comparisons to known viruses. The mammalian viruses included those of the Adenoviridae, Herpesviridae, Papillomaviridae, Retroviridae, Circoviridae, Rhabdoviridae, Astroviridae, Flaviridae, Coronaviridae, Picornaviridae, and Parvovirinae; insect viruses included those of the Baculoviridae, Iflaviridae, Dicistroviridae, Tetraviridae, and Densovirinae; fungal viruses included those of the Chrysoviridae, Hypoviridae, Partitiviridae, and Totiviridae; and phages included those of the Caudovirales, Inoviridae, and Microviridae and unclassified phages. In addition to the viruses and phages associated with the insects, plants, and bacterial flora related to the diet and habitation of bats, we identified the complete or partial genome sequences of 13 novel mammalian viruses. These included herpesviruses, papillomaviruses, a circovirus, a bocavirus, picornaviruses, a pestivirus, and a foamy virus. Pairwise alignments and phylogenetic analyses indicated that these novel viruses showed little genetic similarity with previously reported viruses. This study also revealed a high prevalence and diversity of bat astroviruses and coronaviruses in some provinces. These findings have expanded our understanding of the viromes of bats in China and hinted at the presence of a large variety of unknown mammalian viruses in many common bat species of mainland China.
Related JoVE Video
Inhibitory effects and underlying mechanism of 7-hydroxyflavone phosphate ester in HeLa cells.
PLoS ONE
Show Abstract
Hide Abstract
Chrysin and its phosphate ester have previously been shown to inhibit cell proliferation and induce apoptosis in Hela cells; however, the underlying mechanism remains to be characterized. In the present study, we therefore synthesized diethyl flavon-7-yl phosphate (FP, C(19)H(19)O(6)P) by a simplified Atheron-Todd reaction, and explored its anti-tumor characteristics and mechanisms. Cell proliferation, cell cycle progression and apoptosis were measured by MTS, flow cytometry and terminal deoxynucleotidyl transferase dUTP nick end labeling techniques, respectively in human cervical cancer HeLa cells treated with 7-hydroxyflavone (HF) and FP. p21, proliferating cell nuclear antigen (PCNA) and cAMP levels in Hela cells were analyzed by western blot and radioimmunoassay. Both HF and FP inhibited proliferation and induced apoptosis in HeLa cells via induction of PCNA/p21 expression, cleaved caspase-3/poly (ADP-ribose) polymerase (PARP)-1, elevation of cAMP levels, and cell cycle arrest with accumulation of cells in the G0/G1 fraction. The effects of FP were more potent than those of HF. The interactions of FP with Ca(2+)-calmodulin (CaM) and Ca(2+)-CaM-phosphodiesterase (PDE)1 were explored by electrospray ionization-mass spectrometry and fluorescence spectra. FP, but not HF, formed non-covalent complexes with Ca(2+)-CaM-PDE1, indicating that FP is an inhibitor of PDE1, and resulting in elevated cellular cAMP levels. It is possible that the elevated cAMP levels inhibit growth and induce apoptosis in Hela cells through induction of p21 and cleaved caspase-3/PARP-1 expression, and causing down-regulation of PCNA and cell cycle arrest with accumulation of cells in the G0/G1 and G2/M fractions. In conclusion, FP was shown to be a Ca(2+)-CaM-PDE inhibitor, which might account for its underlying anti-cancer mechanism in HeLa cells. These observations clearly demonstrate the special roles of phosphorylated flavonoids in biological processes, and suggest that FP might represent a potential new drug for the therapy of human cervical carcinoma.
Related JoVE Video
Common changes in global gene expression induced by RNA polymerase inhibitors in Shigella flexneri.
PLoS ONE
Show Abstract
Hide Abstract
Characterization of expression profile of organisms in response to antimicrobials provides important information on the potential mechanism of action of the drugs. The special expression signature can be used to predict whether other drugs act on the same target. Here, the common response of Shigella flexneri to two inhibitors of RNA polymerase was examined using gene expression profiling. Consistent with similar effects of the two drugs, the gene expression profiles indicated that responses of the bacteria to these drugs were roughly the same, with 225 genes affected commonly. Of them, 88 were induced and 137 were repressed. Real-time PCR was performed for selected genes to verify the microarray results. Analysis of the expression data revealed that more than 30% of the plasmid-encoded genes on the array were up-regulated by the antibiotics including virF regulon, other virulence-related genes, and genes responsible for plasmid replication, maintenance, and transfer. In addition, some chromosome-encoded genes involved in virulence and genes acquired from horizontal transfer were also significantly up-regulated. However, the expression of genes encoding the beta-subunit of RNA polymerase was increased moderately. The repressed genes include those that code for products associated with the ribosome, citrate cycle, glycolysis, thiamine biosynthesis, purine metabolism, fructose metabolism, mannose metabolism, and cold shock proteins. This study demonstrates that the two antibiotics induce rapid cessation of RNA synthesis resulting in inhibition of translation components. It also indicates that the production of virulence factors involved in intercellular dissemination, tissue invasion and inflammatory destruction may be enhanced through derepressing horizontal transfer genes by the drugs.
Related JoVE Video
Enzymatic saccharification of dilute acid pretreated eucalyptus chips for fermentable sugar production.
Bioresour. Technol.
Show Abstract
Hide Abstract
Dilute sulfuric acid was used to pretreat eucalyptus chips prior to enzymatic hydrolysis. After both pretreatment and enzymatic hydrolysis processes. Attention is paid to sugar recovery. The maximum total sugars yield (combined xylose and glucose, 47.69g/100g raw material, representing 82% of total sugars in the eucalyptus biomass) was obtained at 160°C, 0.75% acid concentration and 10min residence time, which is consider to be the best reasonable conditions for the dilute acid pretreatment of eucalyptus, corresponding concentrations of acetic acid, HMF, and furfural in the prehydrolysate were about 2.01g/L, 0.13g/L and 1.37g/L, respectively. Under this optimal pretreatment condition, the acid-insoluble lignin recovery in the insoluble solid resulting from enzymatic hydrolysis, was 22.7g/100g raw material, representing 80% of acid-insoluble lignin in the eucalyptus biomass.
Related JoVE Video
Anti-Japanese-encephalitis-viral effects of kaempferol and daidzin and their RNA-binding characteristics.
PLoS ONE
Show Abstract
Hide Abstract
New therapeutic tools and molecular targets are needed for treatment of Japanese encephalitis virus (JEV) infections. JEV requires an ?-1 translational frameshift to synthesize the NS1 protein required for viral neuroinvasiveness. Several flavonoids have been shown to possess antiviral activity in vitro against a wide spectrum of viruses. To date, the antiviral activities of flavonol kaempferol (Kae) and isoflavonoid daidzin (Dai) against JEV have not been described.
Related JoVE Video
Subpopulation analysis of heteroresistance to fluoroquinolone in Mycobacterium tuberculosis isolates from Beijing, China.
J. Clin. Microbiol.
Show Abstract
Hide Abstract
The presence of heteroresistance was represented by 23% of 235 fluoroquinolone (FQ)-resistant Mycobacterium tuberculosis isolates in Beijing, China, from 2008 to 2010. The main mechanism of FQ heteroresistance is due to the segregation of a single M. tuberculosis strain in patients; the majority of isolates with multidrug-resistant tuberculosis contained a mixture of bacterial subpopulations consisting of various mutant types, suggesting that the improper use of FQ is the major cause of FQ resistance.
Related JoVE Video

What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.